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Article: RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia

TitleRNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia
Authors
KeywordsSpliceosomes
Myelodysplastic Syndromes
RNA Splicing Factor
Issue Date2020
PublisherAmerican Association for Cancer Research. The Journal's web site is located at http://clincancerres.aacrjournals.org/
Citation
Clinical Cancer Research, 2020, v. 26 n. 14, p. 3597-3607 How to Cite?
AbstractPURPOSE: RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of splicing factor genes are common in some hematologic cancers but are relatively uncommon in acute myeloid leukemia (AML, < 20% of patients). We examined whether RNA splicing differences exist in AML, even in the absence of splicing factor mutations. EXPERIMENTAL DESIGN: We developed a bioinformatics pipeline to study alternative RNA splicing in RNA-sequencing data from large cohorts of patients with AML. RESULTS: We have identified recurrent differential alternative splicing between patients with poor and good prognosis. These splicing events occurred even in patients without any discernible splicing factor mutations. Alternative splicing recurrently occurred in genes with specific molecular functions, primarily related to protein translation. Developing tools to predict the functional impact of alternative splicing on the translated protein, we discovered that approximately 45% of the splicing events directly affected highly conserved protein domains. Several splicing factors were themselves misspliced and the splicing of their target transcripts were altered. Studying differential gene expression in the same patients, we identified that alternative splicing of protein translation genes in ELN(Adv) patients resulted in the induction of an integrated stress response and upregulation of inflammation-related genes. Finally, using machine learning techniques, we identified a splicing signature of four genes which refine the accuracy of existing risk prognosis schemes and validated it in a completely independent cohort. CONCLUSIONS: Our discoveries therefore identify aberrant alternative splicing as a molecular feature of adverse AML with clinical relevance.See related commentary by Bowman, p. 3503.
Persistent Identifierhttp://hdl.handle.net/10722/290842
ISSN
2023 Impact Factor: 10.0
2023 SCImago Journal Rankings: 4.623
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorAnande, G-
dc.contributor.authorDeshpande, NP-
dc.contributor.authorMareschal, S-
dc.contributor.authorBatcha, AMN-
dc.contributor.authorHampton, HR-
dc.contributor.authorHerold, T-
dc.contributor.authorLehmann, S-
dc.contributor.authorWilkins, MR-
dc.contributor.authorWong, JWH-
dc.contributor.authorUnnikrishnan, A-
dc.contributor.authorPimanda, JE-
dc.date.accessioned2020-11-02T05:47:53Z-
dc.date.available2020-11-02T05:47:53Z-
dc.date.issued2020-
dc.identifier.citationClinical Cancer Research, 2020, v. 26 n. 14, p. 3597-3607-
dc.identifier.issn1078-0432-
dc.identifier.urihttp://hdl.handle.net/10722/290842-
dc.description.abstractPURPOSE: RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of splicing factor genes are common in some hematologic cancers but are relatively uncommon in acute myeloid leukemia (AML, < 20% of patients). We examined whether RNA splicing differences exist in AML, even in the absence of splicing factor mutations. EXPERIMENTAL DESIGN: We developed a bioinformatics pipeline to study alternative RNA splicing in RNA-sequencing data from large cohorts of patients with AML. RESULTS: We have identified recurrent differential alternative splicing between patients with poor and good prognosis. These splicing events occurred even in patients without any discernible splicing factor mutations. Alternative splicing recurrently occurred in genes with specific molecular functions, primarily related to protein translation. Developing tools to predict the functional impact of alternative splicing on the translated protein, we discovered that approximately 45% of the splicing events directly affected highly conserved protein domains. Several splicing factors were themselves misspliced and the splicing of their target transcripts were altered. Studying differential gene expression in the same patients, we identified that alternative splicing of protein translation genes in ELN(Adv) patients resulted in the induction of an integrated stress response and upregulation of inflammation-related genes. Finally, using machine learning techniques, we identified a splicing signature of four genes which refine the accuracy of existing risk prognosis schemes and validated it in a completely independent cohort. CONCLUSIONS: Our discoveries therefore identify aberrant alternative splicing as a molecular feature of adverse AML with clinical relevance.See related commentary by Bowman, p. 3503.-
dc.languageeng-
dc.publisherAmerican Association for Cancer Research. The Journal's web site is located at http://clincancerres.aacrjournals.org/-
dc.relation.ispartofClinical Cancer Research-
dc.subjectSpliceosomes-
dc.subjectMyelodysplastic Syndromes-
dc.subjectRNA Splicing Factor-
dc.titleRNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia-
dc.typeArticle-
dc.identifier.emailWong, JWH: jwhwong@hku.hk-
dc.identifier.authorityWong, JWH=rp02363-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1158/1078-0432.CCR-20-0184-
dc.identifier.pmid32122925-
dc.identifier.scopuseid_2-s2.0-85086699862-
dc.identifier.hkuros318373-
dc.identifier.volume26-
dc.identifier.issue14-
dc.identifier.spage3597-
dc.identifier.epage3607-
dc.identifier.isiWOS:000551370100014-
dc.publisher.placeUnited States-
dc.identifier.issnl1078-0432-

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